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- PDB-3uxo: Crystal Structure of Rat DNA Polymerase Beta Mutator I260Q Apoenzyme -

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Basic information

Entry
Database: PDB / ID: 3uxo
TitleCrystal Structure of Rat DNA Polymerase Beta Mutator I260Q Apoenzyme
ComponentsDNA polymerase beta
KeywordsTRANSFERASE / LYASE / DNA polymerase beta / BER
Function / homology
Function and homology information


Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases ...Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair, gap-filling / spleen development / DNA-(apurinic or apyrimidinic site) lyase / spindle microtubule / response to gamma radiation / base-excision repair / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / in utero embryonic development / microtubule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / inflammatory response / apoptotic process / DNA damage response / enzyme binding / protein-containing complex / DNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGridley, C.L. / Jaeger, J.
CitationJournal: Biochemistry / Year: 2013
Title: Structural Changes in the Hydrophobic Hinge Region Adversely Affect the Activity and Fidelity of the I260Q Mutator DNA Polymerase beta.
Authors: Gridley, C.L. / Rangarajan, S. / Firbank, S. / Dalal, S. / Sweasy, J.B. / Jaeger, J.
History
DepositionDec 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase beta
B: DNA polymerase beta


Theoretical massNumber of molelcules
Total (without water)76,8072
Polymers76,8072
Non-polymers00
Water4,792266
1
A: DNA polymerase beta


Theoretical massNumber of molelcules
Total (without water)38,4041
Polymers38,4041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA polymerase beta


Theoretical massNumber of molelcules
Total (without water)38,4041
Polymers38,4041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.908, 67.400, 82.456
Angle α, β, γ (deg.)90.00, 115.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA polymerase beta /


Mass: 38403.734 Da / Num. of mol.: 2 / Mutation: I260Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Polb / Production host: Escherichia coli (E. coli)
References: UniProt: P06766, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3350, MES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2010
RadiationMonochromator: Cryogenically cooled double crystal monochromator with horizontal focusing sagittal bend second monocrystal with 4:1 magnification ratio and vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.077→48.59 Å / Num. all: 45730 / Num. obs: 45730 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.08-2.193.90.5941.30.594199.7
2.19-2.3240.4751.40.475199.8
2.32-2.4840.2672.80.267199.8
2.48-2.6840.18140.181199.8
2.68-2.9440.1215.50.121199.7
2.94-3.2840.0976.50.097199.5

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERmolecular replacementphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→24.046 Å / SU ML: 0.72 / σ(F): 1.34 / Phase error: 33.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.318 1996 4.45 %
Rwork0.2573 --
obs0.2601 44844 99.58 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.437 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.2666 Å20 Å2-0.1449 Å2
2---4.237 Å2-0 Å2
3---11.5035 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5222 0 0 266 5488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095318
X-RAY DIFFRACTIONf_angle_d1.1957156
X-RAY DIFFRACTIONf_dihedral_angle_d19.7242066
X-RAY DIFFRACTIONf_chiral_restr0.084780
X-RAY DIFFRACTIONf_plane_restr0.006934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15280.3471470.29622981X-RAY DIFFRACTION99
2.1528-2.2110.41410.30663045X-RAY DIFFRACTION100
2.211-2.2760.43381350.35563041X-RAY DIFFRACTION99
2.276-2.34940.39611500.3243046X-RAY DIFFRACTION100
2.3494-2.43330.33791420.27153089X-RAY DIFFRACTION100
2.4333-2.53060.32321350.27123039X-RAY DIFFRACTION100
2.5306-2.64560.34831490.28283076X-RAY DIFFRACTION100
2.6456-2.78490.35261410.2693077X-RAY DIFFRACTION100
2.7849-2.95910.29771420.26533049X-RAY DIFFRACTION100
2.9591-3.18710.33431420.26283074X-RAY DIFFRACTION100
3.1871-3.5070.32251370.26173069X-RAY DIFFRACTION100
3.507-4.01240.33671470.23653093X-RAY DIFFRACTION100
4.0124-5.04750.28181440.22093108X-RAY DIFFRACTION100
5.0475-24.04790.26431440.24673061X-RAY DIFFRACTION97

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